As far as I can see it is updated by the script /usr/sbin/env-update,
which is run by /etc/init.d/bootmisc, which is linked from /etc/runlevels/boot/bootmisc.
I.e. it gets run at every boot (by /sbin/rc by init as written in /etc/inittab).

So far so good, but what does env-update really do?
I wish the (great!) guys at Gentoo could add some man pages to this and other scripts in /usr/sbin and e.g. to /sbin/rc* also. If there is any list of these scripts, and what they do, please let me know. (The "Gentoo Linux 1.0 Init System" does not even mention env-update sadly enough.)

It is fairly easy to understand that it builds the files /etc/profile.env and /etc/ld.conf.so at least.
So, as an answer to your question, I think you should put you stuff in /etc/env.d (as MarkG said).

I guess the number on the files is some kind of startup order, not sure. If I do:
$ echo "KALLE=anka" > /etc/env.d/90kalle
$ env-update
It goes into /etc/profile.env as it shold at least.